`code-annotation` blocks `copy-button`

[mcanouil]

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

As of the current development version, the code-annotation features blocks the code-copy button feature.
This can be observed on https://quarto.org.

1.7.33 works fine.

This is a bug caused by the attempt to fix the code-copy button location:

• 0defb7a
• b3e7925

Steps to reproduce

See the first block where it's not possible to trigger the code-copy button.

---
format: html
code-copy: true
code-annotations: hover
---

```python
# A commented line
print("Hello, World!") # <1>
```

1. This line prints "Hello, World!" to the console.


```python
# A commented line
print("Bye, World!")
```

Actual behavior

No response

Expected behavior

No response

Your environment

No response

Quarto check output

Quarto 99.9.9
[✓] Checking environment information...
      Quarto cache location: /Users/mcanouil/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.3.1: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: 02c53586f0481b9f6c980a87a367371f31459e71
      Path: /Users/mcanouil/Projects/quarto-dev/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: v2025.07
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/mcanouil/Library/TinyTeX/bin/universal-darwin
      Version: 2025

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /Applications/Brave Browser.app/Contents/MacOS/Brave Browser
      Source: QUARTO_CHROMIUM

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.13.2
      Path: /Users/mcanouil/Projects/quarto-dev/quarto-playground/.venv/bin/python3
      Jupyter: 5.8.1
      Kernels: julia-1.11, python3

[✓] Checking Jupyter engine render....OK

(/) Checking R installation...........ℹ R version 4.5.1 (2025-06-13)
! Config '~/.Rprofile' was loaded!
[✓] Checking R installation...........OK
      Version: 4.5.1
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Users/mcanouil/Projects/quarto-dev/quarto-playground/renv/library/macos/R-4.5/aarch64-apple-darwin20
        - /Users/mcanouil/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.5/aarch64-apple-darwin20/4cd76b74
      knitr: 1.50
      rmarkdown: 2.29

[✓] Checking Knitr engine render......OK

[cscheid]

Thanks, I can repro.

[cscheid]

The PR that we should consider reverting is #12787

[mcanouil]

• Wrap code copy button around outer scaffold #13024

Changes the layout which also creates weird things.

I would suggest to revert both and redo a PR with them and additional testing.